4YQCA

Crystal structure of trmd, a m1g37 trna methyltransferase with sam-competitive compounds
Total Genus 72
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
72
sequence length
248
structure length
237
Chain Sequence
SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGDGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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molecule tags Transferase/transferase inhibitor
molecule keywords tRNA (guanine-N(1)-)-methyltransferase
publication title Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
rcsb
source organism Haemophilus influenzae (strain atcc 51907 / dsm 11121 / kw20 / rd)
total genus 72
structure length 237
sequence length 248
ec nomenclature ec 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
pdb deposition date 2015-03-13

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01746 tRNA_m1G_MT tRNA (Guanine-1)-methyltransferase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.1270.20 Mainly Alpha Orthogonal Bundle Trp Operon Repressor; Chain A tRNA(m1g37)methyltransferase, domain 2 4yqcA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yqcA01
4YPZA 4YQ6A 4YQKA 4YQNA 3N4JA 4X3MA 1V6ZA 4YQ8A 1VHKA 3L8UA 1NXZA 3N4KA 1VH0A 3ILKA 3KY7A 4CNDA 3OINA 2YY8A 4KDZA 4YQGA 1MXIA 2HA8A 1O6DA 4YQ2A 4YQAA 4YQIA 2Z0YA 4YVKA 1ZJRA 5FAIA 1X7PA 4IG6A 5D9FA 4CNGA 4YQ4A 5GMBA 2CX8A 1UAKA 4CNFA 4YQQA 4KGNA 3AXZA 4YQTA 3OIJA 1NS5A 3BBHA 4J3CA 4JALA 4H3ZA 5CO4A 3IC6A 4YQRA 2QWVA 3KNUA 3BBEA 1V2XA 4CNEA 5GM8A 2I6DA 4YQ5A 3IEFA 3O7BA 1Z85A 3AI9X 3OIIA 4YQJA 4YQDA 4YPXA 4YQ0A 1P9PA 4JAKA 2QMMA 4YQBA 4YPYA 2V3JA 4YQCA 1TO0A 4H3YA 4MCBA 4YVJA 4RG1A 1UALA 3QUVA 4YQ3A 4YQ7A 4YVGA 4X3LA 1UAJA 2V3KA 4YQPA 3KTYA 4YVIA 4PZKA 4FAKA 1GZ0A 3DCMX 2EGWA 3NK6A 3GYQA 1IPAA 1K3RA 1VHYA 4MCDA 4YPWA 4YQLA 4YQOA 3BBDA 4YQSA 1J85A 1UAMA 4YVHA 3NK7A 4MCCA 2EGVA 4XBOA 5GMCA 3AIAA 1OY5A 3ONPA 2O3AA 4YQ9A 3KW2A 4E8BA 4YQ1A 1X7OA 3E5YA 4L69A
chains in the Genus database with same CATH superfamily
4YPZA 4YQ6A 4YQKA 4YQNA 3N4JA 4X3MA 1V6ZA 4YQ8A 1VHKA 3L8UA 1NXZA 3N4KA 1VH0A 3ILKA 3KY7A 4CNDA 3OINA 2YY8A 4KDZA 4YQGA 1MXIA 2HA8A 1O6DA 4YQ2A 4YQAA 4YQIA 2Z0YA 4JWGA 4YVKA 1JHGA 1ZJRA 1TRRA 1X7PA 5FAIA 4IG6A 5D9FA 4CNGA 3WRPA 4YQ4A 4FMWA 5GMBA 2CX8A 1UAKA 4CNFA 4YQQA 4KGNA 3AXZA 4YQTA 3OIJA 1NS5A 3BBHA 4J3CA 4JALA 4JWJA 4H3ZA 4JWHA 5CO4A 3IC6A 4YQRA 3KORA 2QWVA 3KNUA 3BBEA 1V2XA 4CNEA 5GM8A 2I6DA 4YQ5A 2OZ9R 3IEFA 3SSXN 3O7BA 1Z85A 3AI9X 3OIIA 4YQJA 4YQDA 2XDIA 4YPXA 4YQ0A 1P9PA 4JAKA 2QMMA 4YQBA 4YPYA 2V3JA 1WRPR 4YQCA 1TO0A 1WRTR 4H3YA 4MCBA 4YVJA 4RG1A 1UALA 3QUVA 4YQ3A 4YQ7A 4YVGA 4X3LA 1UAJA 2V3KA 1MI7R 4YQPA 3KTYA 4YVIA 4PZKA 4FAKA 3SSWN 1GZ0A 3DCMX 2EGWA 1ZT9A 3NK6A 3GYQA 1IPAA 1K3RA 1VHYA 1RCSA 4MCDA 4YPWA 4YQLA 3G1CA 4YQOA 3BBDA 4YQSA 1TROA 1J85A 1UAMA 4YVHA 3NK7A 1WRSR 4MCCA 2EGVA 4XBOA 5GMCA 3AIAA 1OY5A 3ONPA 1CO0A 2O3AA 4YQ9A 3KW2A 4E8BA 4YQ1A 4JWFA 1X7OA 3E5YA 4L69A 3FRWA
chains in the Genus database with same CATH topology
4YPZA 4YQ6A 4YQKA 4YQNA 3N4JA 4X3MA 1V6ZA 4YQ8A 1VHKA 3L8UA 1NXZA 3N4KA 1VH0A 3ILKA 3KY7A 4CNDA 3OINA 2YY8A 4KDZA 4YQGA 1MXIA 2HA8A 1O6DA 4YQ2A 4YQAA 4YQIA 2Z0YA 4JWGA 4YVKA 1ZJRA 5FAIA 1X7PA 4IG6A 5D9FA 4CNGA 4YQ4A 4FMWA 5GMBA 2CX8A 1UAKA 4CNFA 4YQQA 4KGNA 3AXZA 4YQTA 3OIJA 1NS5A 3BBHA 4J3CA 4JALA 4JWJA 4H3ZA 4JWHA 5CO4A 3IC6A 4YQRA 2QWVA 3KNUA 3BBEA 1V2XA 4CNEA 5GM8A 2I6DA 4YQ5A 3IEFA 3O7BA 1Z85A 3AI9X 3OIIA 4YQJA 4YQDA 4YPXA 4YQ0A 1P9PA 4JAKA 2QMMA 4YQBA 4YPYA 2V3JA 4YQCA 1TO0A 4H3YA 4MCBA 4YVJA 4RG1A 1UALA 3QUVA 4YQ3A 4YQ7A 4YVGA 4X3LA 1UAJA 2V3KA 4YQPA 3KTYA 4YVIA 4PZKA 4FAKA 1GZ0A 3DCMX 2EGWA 3NK6A 3GYQA 1IPAA 1K3RA 1VHYA 4MCDA 4YPWA 4YQLA 4YQOA 3BBDA 4YQSA 1J85A 1UAMA 4YVHA 3NK7A 4MCCA 2EGVA 4XBOA 5GMCA 3AIAA 1OY5A 3ONPA 2O3AA 4YQ9A 3KW2A 4E8BA 4YQ1A 4JWFA 1X7OA 3E5YA 4L69A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4YPZ A;  4YQ6 A;  4YQK A;  4YQN A;  3N4J A;  4X3M A;  1V6Z A;  4YQ8 A;  1VHK A;  3L8U A;  1NXZ A;  3N4K A;  1VH0 A;  3ILK A;  3KY7 A;  4CND A;  3OIN A;  2YY8 A;  4KDZ A;  4YQG A;  1MXI A;  2HA8 A;  1O6D A;  4YQ2 A;  4YQA A;  4YQI A;  2Z0Y A;  4YVK A;  1ZJR A;  5FAI A;  1X7P A;  4IG6 A;  5D9F A;  4CNG A;  4YQ4 A;  5GMB A;  2CX8 A;  1UAK A;  4CNF A;  4YQQ A;  4KGN A;  3AXZ A;  4YQT A;  3OIJ A;  1NS5 A;  3BBH A;  4J3C A;  4JAL A;  4H3Z A;  5CO4 A;  3IC6 A;  4YQR A;  2QWV A;  3KNU A;  3BBE A;  1V2X A;  4CNE A;  5GM8 A;  2I6D A;  4YQ5 A;  3IEF A;  3O7B A;  1Z85 A;  3AI9 X;  3OII A;  4YQJ A;  4YQD A;  4YPX A;  4YQ0 A;  1P9P A;  4JAK A;  2QMM A;  4YQB A;  4YPY A;  2V3J A;  4YQC A;  1TO0 A;  4H3Y A;  4MCB A;  4YVJ A;  4RG1 A;  1UAL A;  3QUV A;  4YQ3 A;  4YQ7 A;  4YVG A;  4X3L A;  1UAJ A;  2V3K A;  4YQP A;  3KTY A;  4YVI A;  4PZK A;  4FAK A;  1GZ0 A;  3DCM X;  2EGW A;  3NK6 A;  3GYQ A;  1IPA A;  1K3R A;  1VHY A;  4MCD A;  4YPW A;  4YQL A;  4YQO A;  3BBD A;  4YQS A;  1J85 A;  1UAM A;  4YVH A;  3NK7 A;  4MCC A;  2EGV A;  4XBO A;  5GMC A;  3AIA A;  1OY5 A;  3ONP A;  2O3A A;  4YQ9 A;  3KW2 A;  4E8B A;  4YQ1 A;  1X7O A;  3E5Y A;  4L69 A; 
#chains in the Genus database with same CATH topology
 4YPZ A;  4YQ6 A;  4YQK A;  4YQN A;  3N4J A;  4X3M A;  1V6Z A;  4YQ8 A;  1VHK A;  3L8U A;  1NXZ A;  3N4K A;  1VH0 A;  3ILK A;  3KY7 A;  4CND A;  3OIN A;  2YY8 A;  4KDZ A;  4YQG A;  1MXI A;  2HA8 A;  1O6D A;  4YQ2 A;  4YQA A;  4YQI A;  2Z0Y A;  4JWG A;  4YVK A;  1JHG A;  1ZJR A;  1TRR A;  1X7P A;  5FAI A;  4IG6 A;  5D9F A;  4CNG A;  3WRP A;  4YQ4 A;  4FMW A;  5GMB A;  2CX8 A;  1UAK A;  4CNF A;  4YQQ A;  4KGN A;  3AXZ A;  4YQT A;  3OIJ A;  1NS5 A;  3BBH A;  4J3C A;  4JAL A;  4JWJ A;  4H3Z A;  4JWH A;  5CO4 A;  3IC6 A;  4YQR A;  3KOR A;  2QWV A;  3KNU A;  3BBE A;  1V2X A;  4CNE A;  5GM8 A;  2I6D A;  4YQ5 A;  2OZ9 R;  3IEF A;  3SSX N;  3O7B A;  1Z85 A;  3AI9 X;  3OII A;  4YQJ A;  4YQD A;  2XDI A;  4YPX A;  4YQ0 A;  1P9P A;  4JAK A;  2QMM A;  4YQB A;  4YPY A;  2V3J A;  1WRP R;  4YQC A;  1TO0 A;  1WRT R;  4H3Y A;  4MCB A;  4YVJ A;  4RG1 A;  1UAL A;  3QUV A;  4YQ3 A;  4YQ7 A;  4YVG A;  4X3L A;  1UAJ A;  2V3K A;  1MI7 R;  4YQP A;  3KTY A;  4YVI A;  4PZK A;  4FAK A;  3SSW N;  1GZ0 A;  3DCM X;  2EGW A;  1ZT9 A;  3NK6 A;  3GYQ A;  1IPA A;  1K3R A;  1VHY A;  1RCS A;  4MCD A;  4YPW A;  4YQL A;  3G1C A;  4YQO A;  3BBD A;  4YQS A;  1TRO A;  1J85 A;  1UAM A;  4YVH A;  3NK7 A;  1WRS R;  4MCC A;  2EGV A;  4XBO A;  5GMC A;  3AIA A;  1OY5 A;  3ONP A;  1CO0 A;  2O3A A;  4YQ9 A;  3KW2 A;  4E8B A;  4YQ1 A;  4JWF A;  1X7O A;  3E5Y A;  4L69 A;  3FRW A; 
#chains in the Genus database with same CATH homology
 4YPZ A;  4YQ6 A;  4YQK A;  4YQN A;  3N4J A;  4X3M A;  1V6Z A;  4YQ8 A;  1VHK A;  3L8U A;  1NXZ A;  3N4K A;  1VH0 A;  3ILK A;  3KY7 A;  4CND A;  3OIN A;  2YY8 A;  4KDZ A;  4YQG A;  1MXI A;  2HA8 A;  1O6D A;  4YQ2 A;  4YQA A;  4YQI A;  2Z0Y A;  4JWG A;  4YVK A;  1ZJR A;  5FAI A;  1X7P A;  4IG6 A;  5D9F A;  4CNG A;  4YQ4 A;  4FMW A;  5GMB A;  2CX8 A;  1UAK A;  4CNF A;  4YQQ A;  4KGN A;  3AXZ A;  4YQT A;  3OIJ A;  1NS5 A;  3BBH A;  4J3C A;  4JAL A;  4JWJ A;  4H3Z A;  4JWH A;  5CO4 A;  3IC6 A;  4YQR A;  2QWV A;  3KNU A;  3BBE A;  1V2X A;  4CNE A;  5GM8 A;  2I6D A;  4YQ5 A;  3IEF A;  3O7B A;  1Z85 A;  3AI9 X;  3OII A;  4YQJ A;  4YQD A;  4YPX A;  4YQ0 A;  1P9P A;  4JAK A;  2QMM A;  4YQB A;  4YPY A;  2V3J A;  4YQC A;  1TO0 A;  4H3Y A;  4MCB A;  4YVJ A;  4RG1 A;  1UAL A;  3QUV A;  4YQ3 A;  4YQ7 A;  4YVG A;  4X3L A;  1UAJ A;  2V3K A;  4YQP A;  3KTY A;  4YVI A;  4PZK A;  4FAK A;  1GZ0 A;  3DCM X;  2EGW A;  3NK6 A;  3GYQ A;  1IPA A;  1K3R A;  1VHY A;  4MCD A;  4YPW A;  4YQL A;  4YQO A;  3BBD A;  4YQS A;  1J85 A;  1UAM A;  4YVH A;  3NK7 A;  4MCC A;  2EGV A;  4XBO A;  5GMC A;  3AIA A;  1OY5 A;  3ONP A;  2O3A A;  4YQ9 A;  3KW2 A;  4E8B A;  4YQ1 A;  4JWF A;  1X7O A;  3E5Y A;  4L69 A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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